Gene Ontology (GO)
MCDB 187
Monday, January 21, 13 What is the Gene Ontology?
• Set of biological phrases (terms) which are applied to genes: • protein kinase • apoptosis • membrane
Monday, January 21, 13 What is the Gene Ontology?
• Genes are linked, or associated, with GO terms by trained curators at genome databases • known as ‘gene associations’ or GO annotations • Some GO annotations created automatically
Monday, January 21, 13 What is the Gene Ontology?
• Allows biologists to make inferences across large numbers of genes without researching each one individually
Monday, January 21, 13 How does GO work?
• GO is species independent • some terms, especially lower-level, detailed terms may be specific to a certain group • e.g. photosynthesis • But when collapsed up to the higher levels, terms are not dependent on species
Monday, January 21, 13 How does GO work?
What information might we want to capture about a gene product?
• What does the gene product do? • Where and when does it act? • Why does it perform these activities?
Monday, January 21, 13 GO structure
• GO terms divided into three parts: • cellular component • molecular function • biological process
Monday, January 21, 13 Cellular Component
Monday, January 21, 13 Cellular Component
Monday, January 21, 13 Cellular Component
Monday, January 21, 13 Cellular Component
• Enzyme complexes in the component ontology refer to places, not activities.
Monday, January 21, 13 Molecular Function • activities or “jobs” of a gene product
glucose-6-phosphate isomerase activity
Monday, January 21, 13 Molecular Function
insulin binding insulin receptor activity
Monday, January 21, 13 Molecular Function
• A gene product may have several functions; a function term refers to a single reaction or activity, not a gene product. • Sets of functions make up a biological process.
Monday, January 21, 13 Biological Process
a commonly recognized series of events
Monday, January 21, 13 Biological Process
a commonly recognized series of events
cell division
Monday, January 21, 13 Biological Process
transcription
Monday, January 21, 13 Biological Process
regulation of gluconeogenesis
Monday, January 21, 13 Biological Process
limb development
Monday, January 21, 13 Ontology Structure
• Terms are linked by two relationships • is-a • part-of
Monday, January 21, 13 Ontology Structure
cell is-a part-of
membrane chloroplast
mitochondrial chloroplast membrane membrane
Monday, January 21, 13 Ontology Structure
• Ontologies are structured as a hierarchical directed acyclic graph (DAG) • Terms can have more than one parent and zero, one or more children
Monday, January 21, 13 Ontology Structure Directed Acyclic Graph (DAG) - multiple parentage cell allowed
membrane chloroplast
mitochondrial chloroplast membrane membrane
Monday, January 21, 13 Examples of GO structures
Monday, January 21, 13 Examples of GO structures
Monday, January 21, 13 GO tools
• GO resources are freely available to anyone to use without restriction • Includes the ontologies, gene associations and tools developed by GO • Other groups have used GO to create tools for many purposes:
http://www.geneontology.org/GO.tools
Monday, January 21, 13 AmiGO
Monday, January 21, 13 AmiGO
Monday, January 21, 13 AmiGO
Monday, January 21, 13